Application of metabolomics in fungal mediated winery biomass degradation (original) (raw)
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Untargeted Metabolic Profiling of Vitis vinifera during Fungal Degradation
FEMS microbiology letters, 2015
This paper illustrates the application of an untargeted metabolic profiling analysis of winery-derived biomass degraded using four filamentous fungi (Trichoderma harzianum, Aspergillus niger, Penicillium chrysogenum and Penicillium citrinum) and a yeast (Saccharomyces cerevisiae). Analysis of the metabolome resulted in the identification of 233 significant peak features (p<0.05; Fold Change [FC]>2 and signal to noise ratio >50) using gas chromatography-mass spectrometry (GC-MS) followed by statistical chemometric analysis. Furthermore, A. niger and P. chrysogenum produced higher biomass degradation due to considerable β-glucosidase and xylanase activities. The major metabolites generated during fungal degradation which differentiated the metabolic profiles of fungi included sugars, sugar acids, organic acids and fatty acids. Although, P. chrysogenum could degrade hemicelluloses due to its high β-glucosidase and xylanase activities, it could not utilize the resultant pentose...
Biodegradation of winery biomass wastes by developing a symbiotic multi-fungal consortium
2015
Australia is sixth largest global wine grape producer with an annual production of 1.75 million metric tonnes in 2012-13. Owing to its poor digestibility and minor phenolic toxicity, winery waste (about a half of total grape biomass) has limited use as either animal feed or compost fertilizer. During fermentation, Saccharomyces cerevisiae generates about 12-15% ethanol from the raw material, with the residual biomass (approx. 85%) consisting of spent wash, seeds, marcs and pomace generating landfill waste. Publications arising from this thesis work Peer-reviewed journal articles Karpe AV, Harding IH & Palombo EA (2014) Comparative degradation of hydrothermal pretreated winery grape wastes by various fungi. Industrial Crops & Products 59: 228-233 Karpe AV, Beale DJ, Harding IH & Palombo EA (In press) Optimization of degradation of winery-derived biomass wastes by Ascomycetes.
Comparative degradation of grape pomace from winery wastes by various fungal cultures
The fermentation process in wine production yields only 12-15% ethanol from the raw material. The remainder of the raw material (about 85%), including grape seeds, skin, pomace, marcs, stalks and skin pulp, is discarded as landfill waste. Microbes such as fungi not only can reduce BOD and COD levels by about 80-90%, but are also able to degrade the complex biomass into simple biomolecules, many of which can serve as the source of biofuels. In the current study, autoclaved grape pomace was degraded by Trichoderma herzianum, Aspergillus niger, Penicillium notatum and P. citrinum. Chemical quantification was performed for lignins, total soluble sugars (TSS), reducing sugars and pentoses. T. herzianum and P. citrinum cultures displayed increase in lignin content by 54.9% and 54.8%, respectively. None of the fungi was observed to degrade lignin. TSS utilization was up to 48.3% and 45.5% by T. herzianum and A. niger, respectively, while Penicillium species showed 35.8% and 31% utilization...
Metabolomic profiling of non-Saccharomyces yeasts in wine
2016
By submitting this dissertation electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the sole author thereof (save to the extent explicitly otherwise stated) that reproduction and publication thereof by Stellenbosch University will not infringe on any third party rights and that I have not previously in its entirety or in part submitted it for obtaining any qualification.
Microorganisms, 2019
The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast specie...
Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts
Frontiers in Microbiology, 2017
The composition and changes of the fungal population and of the metabolites present in grapes and in ferments of Vitis vinifera L. cv. Corvina, one of the major components of the Amarone musts, were dissected aiming at the identification of constant characteristics possibly influenced by the productive process. The fungal populations and metabolomic profiles were analyzed in three different vintages. 454-pyrosequencing on the ribosomal ITS1 region has been used to identify the fungal population present in Corvina grapes and fresh must. Samples were also subjected to metabolomics analysis measuring both free volatile compounds and glycosylated aroma precursors through an untargeted approach with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Albeit strongly dependent on the climate, both the mycobiota and metabolome of Corvina grapes and fresh musts show some characteristics recursive in different vintages. Such persistent characteristics are likely determined by the method adopted to produce Amarone or other dry wines made from partially dried grapes. In particular, the harsh conditions imposed by the prolonged withering appear to contribute to the shaping of the fungal populations. The fungal genera and metabolites present in different vintages in V. vinifera L. cv. Corvina grapes and fresh musts represent core components of the peculiar technique of production of Amarone. Their identification allows the in-depth understanding and improved control of the process of production of this economically and culturally relevant wine.
Wine microbiology is driven by vineyard and winery anthropogenic factors
Microbial Biotechnology, 2016
The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing-clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non-targeted chemical analysis of musts and wines by FT-ICR-MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO 2 or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO 2 or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted.
Fungal diversity and ecosystem function data from wine fermentation vats and microcosms
Data in Brief, 2016
Grape must is the precursor to wine, and consists of grape juice and its resident microbial community. We used Illumina MiSeq s to track changes in must fungal community composition over time in winery vats and laboratory microcosms. We also measured glucose consumption and biomass in microcosms derived directly from must, and glucose consumption in artificially assembled microcosms. Functional impacts of individual must yeasts in artificially assembled communities were calculated using a "keystone index," developed for "Species richness influences wine ecosystem function through a dominant species" [1]. Community composition data and functional measurements are included in this article. DNA sequences were deposited in GenBank (GenBank: SRP073276). Discussion of must succession and ecosystem functioning in must are provided in [1].
Royal Society Open Science
Lignocellulosic bioethanol production results in huge amounts of stillage, a potentially polluting by-product. Stillage, rich in heavy metals and, mainly, inhibitors, requires specific toxicity studies to be adequately managed. To this purpose, we applied an FTIR ecotoxicological bioassay to evaluate the toxicity of lignocellulosic stillage. Two weak acids and furans, most frequently found in lignocellulosic stillage, have been tested in different mixtures against three Saccharomyces cerevisiae strains. The metabolomic reaction of the test microbes and the mortality induced at various levels of inhibitor concentration showed that the strains are representative of three different types of response. Furthermore, the relationship between concentrations and FTIR synthetic stress indexes has been studied, with the aim of defining a model able to predict the concentrations of inhibitors in stillage, resulting in an optimized predictive model for all the strains. This approach represents a...